X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=21e7b54548a370065ab554d3a2b0f7b5c4887146;hb=0e14094b51dd81c07c6a56b7b51533eff2332339;hp=840eaaccc82c392de096729a5db32d7c72cdf08a;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 840eaac..21e7b54 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -10,7 +10,6 @@
 #include "command.hpp"
 #include "readdistcommand.h"
 #include "readtreecommand.h"
-#include "readsharedcommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
@@ -23,7 +22,6 @@
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
 #include "rarefactsharedcommand.h"
-#include "nocommand.h"
 #include "quitcommand.h"
 #include "helpcommand.h"
 #include "commandfactory.hpp"
@@ -31,7 +29,21 @@
 #include "parsimonycommand.h"
 #include "unifracunweightedcommand.h"
 #include "unifracweightedcommand.h"
-#include <exception>
+#include "libshuffcommand.h"
+#include "heatmapcommand.h"
+#include "filterseqscommand.h"
+#include "mothur.h"
+#include "venncommand.h"
+#include "nocommands.h"
+#include "binsequencecommand.h"
+#include "getoturepcommand.h"
+#include "treegroupscommand.h"
+#include "bootstrapsharedcommand.h"
+#include "concensuscommand.h"
+#include "distancecommand.h"
+#include "aligncommand.h"
+#include "getrepseqscommand.h"
+#include "matrixoutputcommand.h"
 
 
 /***********************************************************/
@@ -40,7 +52,6 @@
 CommandFactory::CommandFactory(){
 	command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -59,7 +70,6 @@ Command* CommandFactory::getCommand(string commandName){
 			 if(commandName == "read.dist")				{	command = new ReadDistCommand();			}
 		else if(commandName == "read.otu")				{	command = new ReadOtuCommand();				}
 		else if(commandName == "read.tree")				{	command = new ReadTreeCommand();			}
-		else if(commandName == "read.shared")			{	command = new ReadSharedCommand();			}
 		else if(commandName == "cluster")				{	command = new ClusterCommand();				}
 		else if(commandName == "deconvolute")			{	command = new DeconvoluteCommand();			}
 		else if(commandName == "parsimony")				{	command = new ParsimonyCommand();			}
@@ -73,9 +83,22 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "summary.shared")		{	command = new SummarySharedCommand();		}
 		else if(commandName == "unifrac.weighted")		{	command = new UnifracWeightedCommand();		}
 		else if(commandName == "unifrac.unweighted")	{	command = new UnifracUnweightedCommand();	}
-		else if(commandName == "get.group")             {   command = new GetgroupCommand();        }
-		else if(commandName == "get.label")             {   command = new GetlabelCommand();        }
-		else if(commandName == "get.line")              {   command = new GetlineCommand();         }
+		else if(commandName == "get.group")             {   command = new GetgroupCommand();			}
+		else if(commandName == "get.label")             {   command = new GetlabelCommand();			}
+		else if(commandName == "get.line")              {   command = new GetlineCommand();				}
+		else if(commandName == "libshuff")              {   command = new LibShuffCommand();			}
+		else if(commandName == "heatmap")				{   command = new HeatMapCommand();				}
+		else if(commandName == "filter.seqs")			{   command = new FilterSeqsCommand();          }
+		else if(commandName == "venn")					{   command = new VennCommand();				}
+		else if(commandName == "bin.seqs")				{   command = new BinSeqCommand();				}
+		else if(commandName == "get.repseqs")			{   command = new GetRepSeqsCommand();			}
+		else if(commandName == "get.oturep")			{   command = new GetOTURepCommand();			}
+		else if(commandName == "tree.shared")			{   command = new TreeGroupCommand();			}
+		else if(commandName == "dist.shared")			{   command = new MatrixOutputCommand();		}
+		else if(commandName == "bootstrap.shared")		{   command = new BootSharedCommand();			}
+		else if(commandName == "concensus")				{   command = new ConcensusCommand();			}
+		else if(commandName == "dist.seqs")				{   command = new DistanceCommand();			}
+		else if(commandName == "align.seqs")			{   command = new AlignCommand();				}
 		else											{	command = new NoCommand();					}
 
 		return command;